GHA: trigger CI workflow on merge_group event #84
Workflow file for this run
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| name: CI | ||
| # trigger | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - develop | ||
| pull_request: | ||
| workflow_dispatch: | ||
| merge_queue: | ||
| schedule: | ||
| # run Monday and Thursday at 03:42 UTC | ||
| - cron: '42 3 * * MON,THU' | ||
| env: | ||
| # use all available cores for compiling amici models | ||
| AMICI_PARALLEL_COMPILE: "" | ||
| # non-interactive backend for matplotlib | ||
| MPLBACKEND: "agg" | ||
| # jobs | ||
| jobs: | ||
| base: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10', '3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici | ||
| - name: Run tests | ||
| timeout-minutes: 30 | ||
| run: tox -e base | ||
| env: | ||
| CC: clang | ||
| CXX: clang++ | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| mac: | ||
| runs-on: macos-13 # TODO: change to macos-latest after the next release | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici | ||
| - name: Run tests | ||
| timeout-minutes: 30 | ||
| run: ulimit -n 65536 65536 && tox -e base | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| windows: | ||
| runs-on: windows-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~\AppData\Local\pip\Cache | ||
| .tox | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: | | ||
| pip install --upgrade pip | ||
| pip install tox | ||
| - name: Run tests | ||
| shell: bash | ||
| timeout-minutes: 10 | ||
| run: tox -e windows | ||
| petab: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10', '3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici pysb | ||
| - name: Run tests | ||
| timeout-minutes: 35 | ||
| run: tox -e petab | ||
| env: | ||
| CC: clang | ||
| CXX: clang++ | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| julia: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10', '3.12'] | ||
| # needed to allow julia-actions/cache to delete old caches that it has created | ||
| permissions: | ||
| actions: write | ||
| contents: read | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache tox and cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install julia | ||
| uses: julia-actions/setup-julia@v2 | ||
| with: | ||
| version: 1.9 | ||
| - name: Cache Julia | ||
| uses: julia-actions/cache@v2 | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh | ||
| - name: Install PEtabJL dependencies | ||
| run: > | ||
| julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0")); | ||
| Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")' | ||
| - name: Run tests | ||
| timeout-minutes: 25 | ||
| run: tox -e julia | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| optimize: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh ipopt | ||
| - name: Run tests | ||
| timeout-minutes: 25 | ||
| run: tox -e optimize | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| hierarchical: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10', '3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici | ||
| - name: Run tests | ||
| timeout-minutes: 20 | ||
| run: tox -e hierarchical | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| select: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10', '3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici | ||
| - name: Run tests | ||
| timeout-minutes: 20 | ||
| run: tox -e select | ||
| - name: Coverage | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| file: ./coverage.xml | ||
| quality: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.12'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: pip install tox pre-commit | ||
| - name: Check repository size | ||
| run: tox -e size | ||
| - name: Run pre-commit hooks | ||
| run: pre-commit run --all-files | ||
| docs: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.11'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh doc amici | ||
| - name: Validate CITATION.cff | ||
| run: pip install cffconvert && cffconvert --validate | ||
| - name: Build doc | ||
| timeout-minutes: 30 | ||
| run: tox -e doc | ||
| notebooks1: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici ipopt | ||
| - name: Run notebooks 1 | ||
| timeout-minutes: 20 | ||
| run: tox -e notebooks1 | ||
| notebooks2: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.10'] | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@v4 | ||
| - name: Prepare python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.cache/pip | ||
| .tox/ | ||
| key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | ||
| - name: Install dependencies | ||
| run: .github/workflows/install_deps.sh amici | ||
| - name: Run notebooks 2 | ||
| timeout-minutes: 20 | ||
| run: tox -e notebooks2 | ||
